webservices/compbio/ws/client/Jws2Client.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.ws.client;\r
  20 \r
  21 import static compbio.ws.client.Constraints.inputkey;\r
  22 import static compbio.ws.client.Constraints.outputkey;\r
  23 import static compbio.ws.client.Constraints.paramFile;\r
  24 \r
  25 import java.io.Closeable;\r
  26 import java.io.File;\r
  27 import java.io.FileInputStream;\r
  28 import java.io.IOException;\r
  29 import java.io.PrintWriter;\r
  30 import java.io.Writer;\r
  31 import java.net.ConnectException;\r
  32 import java.net.MalformedURLException;\r
  33 import java.net.URL;\r
  34 import java.util.Arrays;\r
  35 import java.util.Collections;\r
  36 import java.util.List;\r
  37 import java.util.Set;\r
  38 import java.util.logging.Level;\r
  39 import java.util.logging.Logger;\r
  40 \r
  41 import javax.xml.namespace.QName;\r
  42 import javax.xml.ws.Service;\r
  43 import javax.xml.ws.WebServiceException;\r
  44 \r
  45 import compbio.data.msa.JABAService;\r
  46 import compbio.data.msa.FoldWS;\r
  47 import compbio.data.msa.Metadata;\r
  48 import compbio.data.msa.MsaWS;\r
  49 import compbio.data.msa.RegistryWS;\r
  50 import compbio.data.msa.SequenceAnnotation;\r
  51 import compbio.data.sequence.Alignment;\r
  52 import compbio.data.sequence.FastaSequence;\r
  53 import compbio.data.sequence.ScoreManager;\r
  54 import compbio.data.sequence.ClustalAlignmentUtil;\r
  55 import compbio.data.sequence.SequenceUtil;\r
  56 import compbio.data.sequence.UnknownFileFormatException;\r
  57 import compbio.metadata.JobSubmissionException;\r
  58 import compbio.metadata.Option;\r
  59 import compbio.metadata.Preset;\r
  60 import compbio.metadata.ResultNotAvailableException;\r
  61 import compbio.metadata.WrongParameterException;\r
  62 import compbio.util.FileUtil;\r
  63 \r
  64 /**\r
  65  * A command line client for JAva Bioinformatics Analysis Web Services\r
  66  * \r
  67  * @author pvtroshin\r
  68  * @version 1.0\r
  69  */\r
  70 public class Jws2Client {\r
  71 \r
  72         /*\r
  73          * Use java.util.Logger instead of log4j logger to reduce the size of the\r
  74          * client package\r
  75          */\r
  76         private static final Logger log = Logger.getLogger(Jws2Client.class\r
  77                         .getCanonicalName());\r
  78 \r
  79         /**\r
  80          * Attempt to construct the URL object from the string\r
  81          * \r
  82          * @param urlstr\r
  83          * @return true if it succeed false otherwise\r
  84          */\r
  85         public static boolean validURL(String urlstr) {\r
  86                 try {\r
  87                         if (urlstr == null || urlstr.trim().length() == 0) {\r
  88                                 return false;\r
  89                         }\r
  90                         new URL(urlstr);\r
  91                 } catch (MalformedURLException e) {\r
  92                         return false;\r
  93                 }\r
  94                 return true;\r
  95         }\r
  96 \r
  97         /**\r
  98          * Connects to the service and do the job as requested, if something goes\r
  99          * wrong reports or/and prints usage help.\r
 100          * \r
 101          * @param <T>\r
 102          *            web service type\r
 103          * @param cmd\r
 104          *            command line options\r
 105          * @throws IOException\r
 106          */\r
 107         <T> Jws2Client(String[] cmd) throws IOException {\r
 108                 \r
 109 \r
 110                 String hostname = CmdHelper.getHost(cmd);\r
 111                 if (hostname == null) {\r
 112                         System.err.println("Host name is not provided!");\r
 113                         printUsage(1);\r
 114                 }\r
 115 \r
 116                 if (!validURL(hostname)) {\r
 117                         System.err.println("Host name is not valid!");\r
 118                         printUsage(1);\r
 119                 }\r
 120                 // Just list available services and quit\r
 121                 boolean listServices = CmdHelper.listServices(cmd);\r
 122                 if (listServices) {\r
 123                         listServices(hostname);\r
 124                         System.exit(0);\r
 125                 }\r
 126 \r
 127                 String serviceName = CmdHelper.getServiceName(cmd);\r
 128                 if (serviceName == null) {\r
 129                         System.err.println("Service name is no provided!");\r
 130                         printUsage(1);\r
 131                 }\r
 132                 Services service = Services.getService(serviceName);\r
 133                 if (service == null) {\r
 134                         System.err.println("Service " + serviceName\r
 135                                         + " is no recognized! Valid values are: "\r
 136                                         + Arrays.toString(Services.values()));\r
 137                         printUsage(1);\r
 138                 }\r
 139                 // Test service and quit\r
 140                 boolean testService = CmdHelper.testService(cmd);\r
 141                 if (testService) {\r
 142                         testService(hostname, service, new PrintWriter(System.out, true));\r
 143                         System.exit(0);\r
 144                 }\r
 145 \r
 146                 File inputFile = IOHelper.getFile(cmd, inputkey, true);\r
 147                 File outFile = IOHelper.getFile(cmd, outputkey, false);\r
 148                 File parametersFile = IOHelper.getFile(cmd, paramFile, true);\r
 149                 String presetName = CmdHelper.getPresetName(cmd);\r
 150 \r
 151                 Metadata<T> msaws = (Metadata<T>) connect(hostname, service);\r
 152                 Preset<T> preset = null;\r
 153                 if (presetName != null) {\r
 154                         preset = MetadataHelper.getPreset(msaws, presetName);\r
 155                 }\r
 156                 List<Option<T>> customOptions = null;\r
 157                 if (parametersFile != null) {\r
 158                         List<String> prms = IOHelper.loadParameters(parametersFile);\r
 159                         customOptions = MetadataHelper.processParameters(prms,\r
 160                                         msaws.getRunnerOptions());\r
 161                 }\r
 162 //              System.out.println("The Options read from the command line: " + customOptions);\r
 163                 \r
 164                 Alignment alignment = null;\r
 165                 if (inputFile != null) {\r
 166                         Writer writer = null;\r
 167                         if (outFile != null) {\r
 168                                 writer = IOHelper.getWriter(outFile);\r
 169                         } else {\r
 170                                 // this stream is going to be closed later which is fine as\r
 171                                 // std.out will not be\r
 172                                 writer = new PrintWriter(System.out, true);\r
 173                         }\r
 174                         if (service.getServiceType() == SequenceAnnotation.class) {\r
 175                                 ScoreManager result = analize(inputFile,\r
 176                                                 ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
 177 \r
 178                                 // A System.out.println just for testing!\r
 179                                 System.out.println(result.toString());\r
 180                                 \r
 181                                 IOHelper.writeOut(writer, result);\r
 182                         } else if (service.getServiceType() == MsaWS.class) {\r
 183                                 alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
 184                                                 customOptions);\r
 185                                 IOHelper.writeOut(writer, alignment);\r
 186                         }\r
 187                         writer.close();\r
 188                 }\r
 189 \r
 190                 boolean listParameters = CmdHelper.listParameters(cmd);\r
 191                 if (listParameters) {\r
 192                         System.out.println(MetadataHelper.getParametersList(msaws));\r
 193                 }\r
 194                 boolean listPreset = CmdHelper.listPresets(cmd);\r
 195                 if (listPreset) {\r
 196                         System.out.println(MetadataHelper.getPresetList(msaws));\r
 197                 }\r
 198                 boolean listLimits = CmdHelper.listLimits(cmd);\r
 199                 if (listLimits) {\r
 200                         System.out.println(MetadataHelper.getLimits(msaws));\r
 201                 }\r
 202                 log.fine("Disconnecting...");\r
 203                 ((Closeable) msaws).close();\r
 204                 log.fine("Disconnected successfully!");\r
 205         }\r
 206 \r
 207         /**\r
 208          * Asks registry to test the service on the host hostname\r
 209          * \r
 210          * @param hostname\r
 211          * @param service\r
 212          * @param writer\r
 213          * @throws ConnectException\r
 214          * @throws WebServiceException\r
 215          */\r
 216         public static void testService(String hostname, Services service,\r
 217                         PrintWriter writer) throws ConnectException, WebServiceException {\r
 218                 RegistryWS registry = connectToRegistry(hostname);\r
 219                 if (registry != null) {\r
 220                         String message = registry.testService(service);\r
 221                         writer.println("Service " + service + " testing results: ");\r
 222                         writer.println(message);\r
 223                         FileUtil.closeSilently(((Closeable) registry));\r
 224                 }\r
 225                 writer.flush();\r
 226         }\r
 227 \r
 228         public static Set<Services> getServices(String hostname)\r
 229                         throws WebServiceException, ConnectException {\r
 230                 RegistryWS registry = connectToRegistry(hostname);\r
 231                 Set<Services> services = Collections.EMPTY_SET;\r
 232                 if (registry != null) {\r
 233                         services = registry.getSupportedServices();\r
 234                         FileUtil.closeSilently(((Closeable) registry));\r
 235                 }\r
 236                 return services;\r
 237         }\r
 238 \r
 239         private static void listServices(String hostname)\r
 240                         throws WebServiceException, IOException {\r
 241                 Set<Services> services = Jws2Client.getServices(hostname);\r
 242                 if (!services.isEmpty()) {\r
 243                         System.out.println("Supported services are: "\r
 244                                         + Services.toString(services));\r
 245                 } else {\r
 246                         System.out.println("Failed to connect to the registry! ");\r
 247                 }\r
 248         }\r
 249 \r
 250         /**\r
 251          * Calculate conservation for sequences loaded from the file\r
 252          * \r
 253          * @param wsproxy\r
 254          *            a web service proxy\r
 255          * @param file\r
 256          *            the file to read the results from\r
 257          * @param preset\r
 258          *            Preset to use optional\r
 259          * @param customOptions\r
 260          *            the list of options\r
 261          * @return Set<Score> the conservation scores\r
 262          * @throws UnknownFileFormatException\r
 263          */\r
 264         static <T> ScoreManager analize(List<FastaSequence> fastalist,\r
 265                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 266                         List<Option<T>> customOptions) {\r
 267 \r
 268                 ScoreManager scores = null;\r
 269                 try {\r
 270                         String jobId = null;\r
 271                         if (customOptions != null && preset != null) {\r
 272                                 System.out\r
 273                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 274                         }\r
 275                         if (customOptions != null) {\r
 276                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 277                         } else if (preset != null) {\r
 278                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 279                         } else {\r
 280                                 jobId = wsproxy.analize(fastalist);\r
 281                         }\r
 282                         System.out.println("\n\ncalling analise.........");\r
 283                         Thread.sleep(1000);\r
 284                         scores = wsproxy.getAnnotation(jobId);\r
 285 \r
 286                 } catch (JobSubmissionException e) {\r
 287                         System.err\r
 288                                         .println("Exception while submitting job to a web server. "\r
 289                                                         + "Exception details are below:");\r
 290                         e.printStackTrace();\r
 291                 } catch (ResultNotAvailableException e) {\r
 292                         System.err.println("Exception while waiting for results. "\r
 293                                         + "Exception details are below:");\r
 294                         e.printStackTrace();\r
 295                 } catch (InterruptedException e) {\r
 296                         // ignore and propagate an interruption\r
 297                         Thread.currentThread().interrupt();\r
 298                         System.err.println("Exception while waiting for results. "\r
 299                                         + "Exception details are below:");\r
 300                         e.printStackTrace();\r
 301                 } catch (WrongParameterException e) {\r
 302                         System.err\r
 303                                         .println("Exception while parsing the web method input parameters. "\r
 304                                                         + "Exception details are below:");\r
 305                         e.printStackTrace();\r
 306                 }\r
 307                 return scores;\r
 308 \r
 309         }\r
 310 \r
 311         /**\r
 312          * Calculate conservation for sequences loaded from the file\r
 313          * \r
 314          * @param wsproxy\r
 315          *            a web service proxy\r
 316          * @param file\r
 317          *            the file to read the results from\r
 318          * @param preset\r
 319          *            Preset to use optional\r
 320          * @param customOptions\r
 321          *            the list of options\r
 322          * @return Set<Score> the conservation scores\r
 323          * @throws IOException\r
 324          * @throws UnknownFileFormatException\r
 325          */\r
 326         static <T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy,\r
 327                         Preset<T> preset, List<Option<T>> customOptions) {\r
 328                 List<FastaSequence> fastalist = null;\r
 329                 try {\r
 330                         fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 331                         assert !fastalist.isEmpty() : "Input is empty!";\r
 332                 } catch (IOException e) {\r
 333                         System.err\r
 334                                         .println("Exception while reading the input file. "\r
 335                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 336                                                         + "Exception details are below:");\r
 337                         e.printStackTrace();\r
 338                 } catch (UnknownFileFormatException e) {\r
 339                         System.err\r
 340                                         .println("Exception while attempting to read the input file "\r
 341                                                         + "Exception details are below:");\r
 342                         System.out.println(e.getMessage());\r
 343                         e.printStackTrace();\r
 344                 }\r
 345                 return analize(fastalist, wsproxy, preset, customOptions);\r
 346         }\r
 347         /**\r
 348          * Connects to a web service by the host and the service name web service\r
 349          * type\r
 350          * \r
 351          * @param host\r
 352          *            the fully qualified name of JABAWS server including JABAWS\r
 353          *            context name e.g\r
 354          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 355          * @param service\r
 356          *            the name of the JABAWS service to connect to\r
 357          * @return JABAService<T>\r
 358          * @throws WebServiceException\r
 359          * @throws ConnectException\r
 360          *             if fails to connect to the service on the host\r
 361          */\r
 362         public static JABAService connect(String host, Services service)\r
 363                         throws WebServiceException, ConnectException {\r
 364                 URL url = null;\r
 365                 log.log(Level.FINE, "Attempting to connect...");\r
 366                 try {\r
 367                         url = new URL(host + "/" + service.toString() + "?wsdl");\r
 368                 } catch (MalformedURLException e) {\r
 369                         e.printStackTrace();\r
 370                         // ignore as the host name is already verified\r
 371                 }\r
 372                 Service serv = null;\r
 373                 try {\r
 374                         serv = service.getService(url, JABAService.SERVICE_NAMESPACE);\r
 375                 } catch (WebServiceException wse) {\r
 376                         System.out.println("Connecting to JABAWS version 2 service");\r
 377                         if (isV2service(wse)) {\r
 378                                 serv = service\r
 379                                                 .getService(url, JABAService.V2_SERVICE_NAMESPACE);\r
 380                         }\r
 381                 }\r
 382                 if (serv == null) {\r
 383                         throw new ConnectException("Could not connect to " + url\r
 384                                         + " the server is down?");\r
 385                 }\r
 386                 JABAService serviceIF = service.getInterface(serv);\r
 387                 log.log(Level.INFO, "Connected successfully!");\r
 388 \r
 389                 return serviceIF;\r
 390         }\r
 391 \r
 392         static boolean isV2service(WebServiceException wse) {\r
 393                 String message = wse.getMessage();\r
 394                 int idx = message.indexOf("not a valid service");\r
 395                 if (idx > 0) {\r
 396                         if (message.substring(idx).contains(\r
 397                                         JABAService.V2_SERVICE_NAMESPACE)) {\r
 398                                 return true;\r
 399                         }\r
 400                 }\r
 401                 return false;\r
 402         }\r
 403 \r
 404         /**\r
 405          * Get a connection of JABAWS registry\r
 406          * \r
 407          * @param host\r
 408          *            the fully qualified name of JABAWS server including JABAWS\r
 409          *            context name e.g\r
 410          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 411          * @return compbio.data.msa.RegistryWS - instance of a RegistryWS web\r
 412          *         service\r
 413          * @throws WebServiceException\r
 414          * @throws ConnectException\r
 415          */\r
 416         public static compbio.data.msa.RegistryWS connectToRegistry(String host)\r
 417                         throws WebServiceException, ConnectException {\r
 418                 URL url = null;\r
 419                 String service = "RegistryWS";\r
 420                 log.log(Level.FINE, "Attempting to connect...");\r
 421 \r
 422                 try {\r
 423                         url = new URL(host + "/" + service + "?wsdl");\r
 424                 } catch (MalformedURLException e) {\r
 425                         e.printStackTrace();\r
 426                         // ignore as the host name is already verified\r
 427                 }\r
 428                 QName qname = new QName(JABAService.V2_SERVICE_NAMESPACE, service);\r
 429                 Service serv = Service.create(url, qname);\r
 430 \r
 431                 if (serv == null) {\r
 432                         throw new ConnectException("Could not connect to " + url\r
 433                                         + " the server is down?");\r
 434                 }\r
 435 \r
 436                 QName portName = new QName(serv.getServiceName().getNamespaceURI(),\r
 437                                 service + "Port");\r
 438                 compbio.data.msa.RegistryWS serviceIF = serv.getPort(portName,\r
 439                                 compbio.data.msa.RegistryWS.class);\r
 440 \r
 441                 log.log(Level.INFO, "Connected to " + service + " successfully!");\r
 442 \r
 443                 return serviceIF;\r
 444         }\r
 445 \r
 446         /**\r
 447          * Align sequences from the file using MsaWS\r
 448          * \r
 449          * @param <T>\r
 450          *            web service type e.g. Clustal\r
 451          * @param file\r
 452          *            to write the resulting alignment to\r
 453          * @param msaws\r
 454          *            MsaWS required\r
 455          * @param preset\r
 456          *            Preset to use optional\r
 457          * @param customOptions\r
 458          *            file which contains new line separated list of options\r
 459          * @return Alignment\r
 460          */\r
 461         static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
 462                         List<Option<T>> customOptions) {\r
 463                 FileInputStream instream = null;\r
 464                 List<FastaSequence> fastalist = null;\r
 465                 Alignment alignment = null;\r
 466                 try {\r
 467                         instream = new FileInputStream(file);\r
 468                         fastalist = SequenceUtil.readFasta(instream);\r
 469                         instream.close();\r
 470                         String jobId = null;\r
 471                         if (customOptions != null && preset != null) {\r
 472                                 System.out\r
 473                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 474                         }\r
 475                         if (customOptions != null) {\r
 476                                 jobId = msaws.customAlign(fastalist, customOptions);\r
 477                         } else if (preset != null) {\r
 478                                 jobId = msaws.presetAlign(fastalist, preset);\r
 479                         } else {\r
 480                                 jobId = msaws.align(fastalist);\r
 481                         }\r
 482                         System.out.println("\n\ncalling align.........");\r
 483                         Thread.sleep(1000);\r
 484                         alignment = msaws.getResult(jobId);\r
 485 \r
 486                 } catch (IOException e) {\r
 487                         System.err\r
 488                                         .println("Exception while reading the input file. "\r
 489                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 490                                                         + "Exception details are below:");\r
 491                         e.printStackTrace();\r
 492                 } catch (JobSubmissionException e) {\r
 493                         System.err\r
 494                                         .println("Exception while submitting job to a web server. "\r
 495                                                         + "Exception details are below:");\r
 496                         e.printStackTrace();\r
 497                 } catch (ResultNotAvailableException e) {\r
 498                         System.err.println("Exception while waiting for results. "\r
 499                                         + "Exception details are below:");\r
 500                         e.printStackTrace();\r
 501                 } catch (InterruptedException ignored) {\r
 502                         // ignore and propagate an interruption\r
 503                         Thread.currentThread().interrupt();\r
 504                 } catch (WrongParameterException e) {\r
 505                         e.printStackTrace();\r
 506                 } finally {\r
 507                         if (instream != null) {\r
 508                                 try {\r
 509                                         instream.close();\r
 510                                 } catch (IOException ignored) {\r
 511                                         // ignore\r
 512                                 }\r
 513                         }\r
 514                 }\r
 515                 return alignment;\r
 516         }\r
 517         \r
 518         /**\r
 519          * Return RNA secondary structure from a file using FoldWS\r
 520          * \r
 521          * @param <T>\r
 522          *            web service type e.g. Clustal\r
 523          * @param file\r
 524          *            to read the results from\r
 525          * @param foldws\r
 526          *            FoldWS required\r
 527          * @param preset\r
 528          *            Preset to use optional\r
 529          * @param customOptions\r
 530          *            file which contains new line separated list of options\r
 531          * @return String\r
 532          */\r
 533         \r
 534 //      static <T> String fold(File file, FoldWS<T> foldws, Preset<T> preset,\r
 535 //                      List<Option<T>> customOptions) {\r
 536 //              FileInputStream instream = null;\r
 537 //              Alignment alignment = null;\r
 538 //              String rnastruct = null;\r
 539 //              try {\r
 540 //                      instream = new FileInputStream(file);\r
 541 //                      alignment = ClustalAlignmentUtil.readClustalFile(instream);\r
 542 //                      instream.close();\r
 543 //                      String jobId = null;\r
 544 //                      if (customOptions != null && preset != null) {\r
 545 //                              System.out.println("WARN: Parameters (-f) are defined together"\r
 546 //                                              + "with a preset (-r), ignoring preset! ");\r
 547 //                      }\r
 548 //                      if (customOptions != null) {\r
 549 //                              jobId = foldws.customFold(alignment, customOptions);\r
 550 //                      } else if (preset != null) {\r
 551 //                              jobId = foldws.presetFold(alignment, preset);\r
 552 //                      } else {\r
 553 //                              jobId = foldws.fold(alignment);\r
 554 //                      }\r
 555 //                      System.out.println("\n\ncalling fold.........");\r
 556 //                      Thread.sleep(1000);\r
 557 //                      rnastruct = foldws.getResult(jobId);\r
 558 //                              \r
 559 //              } catch (IOException e) {\r
 560 //                      System.err.println("Exception while reading the input file. Exception details: ");\r
 561 //                      e.printStackTrace();\r
 562 //              } catch (UnknownFileFormatException e) {\r
 563 //                      System.err.println("Exception while reading input file. Doesnt look like a Clustal format file");\r
 564 //                      e.printStackTrace();\r
 565 //              } catch (JobSubmissionException e) {\r
 566 //                      System.err.println("Exception while submitting job to the web server. ");\r
 567 //                      e.printStackTrace();\r
 568 //              } catch (ResultNotAvailableException e) {\r
 569 //                      System.err.println("Exception while waiting for results. Exception details: ");\r
 570 //                      e.printStackTrace();\r
 571 //              } catch (InterruptedException ignored) {\r
 572 //                      // ignore and propagate an interruption\r
 573 //                      Thread.currentThread().interrupt();\r
 574 //              } catch (WrongParameterException e) {\r
 575 //                      e.printStackTrace();\r
 576 //              } finally {\r
 577 //                      if (instream != null) {\r
 578 //                              try {\r
 579 //                                      instream.close();\r
 580 //                              } catch (IOException ignored) {\r
 581 //                                      // ignore\r
 582 //                              }\r
 583 //                      }\r
 584 //              }\r
 585 //              return rnastruct;\r
 586 //      }\r
 587 //              \r
 588         /**\r
 589          * Prints Jws2Client usage information to standard out\r
 590          * \r
 591          * @param exitStatus\r
 592          */\r
 593         static void printUsage(int exitStatus) {\r
 594                 System.out.println(Constraints.help_text);\r
 595                 System.exit(exitStatus);\r
 596         }\r
 597 \r
 598         /**\r
 599          * Starts command line client, if no parameter are supported print help. Two\r
 600          * parameters are required for successful call the JWS2 host name and a\r
 601          * service name.\r
 602          * \r
 603          * @param args\r
 604          *            Usage: <Class or Jar file name> -h=host_and_context\r
 605          *            -s=serviceName ACTION [OPTIONS]\r
 606          * \r
 607          *            -h=<host_and_context> - a full URL to the JWS2 web server\r
 608          *            including context path e.g. http://10.31.1.159:8080/ws\r
 609          * \r
 610          *            -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,\r
 611          *            TcoffeeWS, ProbconsWS] ACTIONS:\r
 612          * \r
 613          *            -i=<inputFile> - full path to fasta formatted sequence file,\r
 614          *            from which to align sequences\r
 615          * \r
 616          *            -parameters - lists parameters supported by web service\r
 617          * \r
 618          *            -presets - lists presets supported by web service\r
 619          * \r
 620          *            -limits - lists web services limits Please note that if input\r
 621          *            file is specified other actions are ignored\r
 622          * \r
 623          *            OPTIONS: (only for use with -i action):\r
 624          * \r
 625          *            -r=<presetName> - name of the preset to use\r
 626          * \r
 627          *            -o=<outputFile> - full path to the file where to write an\r
 628          *            alignment -f=<parameterInputFile> - the name of the file with\r
 629          *            the list of parameters to use. Please note that -r and -f\r
 630          *            options cannot be used together. Alignment is done with either\r
 631          *            preset or a parameters from the file, but not both!\r
 632          * \r
 633          */\r
 634         public static void main(String[] args) {\r
 635 \r
 636                 if (args == null) {\r
 637                         printUsage(1);\r
 638                 }\r
 639                 if (args.length < 2) {\r
 640                         System.err.println("Host and service names are required!");\r
 641                         printUsage(1);\r
 642                 }\r
 643 \r
 644                 try {\r
 645                         new Jws2Client(args);\r
 646                 } catch (IOException e) {\r
 647                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(),\r
 648                                         e.getCause());\r
 649                         System.err.println("Cannot write output file! Stack trace: ");\r
 650                         e.printStackTrace();\r
 651                 }\r
 652         }\r
 653 }\r